Preemptible-based scaffold hopping

ABSTRACT

In a method of molecular scaffold hopping an interface of a scheduler computer sends instructions, prepared by the scheduler computer, to a job runner computer to perform a plurality of separate computational tasks. Each of the separate computational tasks includes calculating one or more chemical properties for a query molecule or molecules in a library of molecules. One or more of the plurality of separate computational tasks performed on the job runner computer are preemptible computing instances. Status indicators sent from the job runner computer are received by the interface for each of the plurality of separate computational tasks. The indicators are one of: incomplete, completed, or failed computing instances. The interface resends the instructions to the job runner computer that correspond to the separate computational tasks having the failed computing instance indicator to increase fault-tolerance against the separate computational tasks not attaining the completed computing instance indicator.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation application of and claims priority toand benefit of co-pending U.S. patent application Ser. No. 16/933,225filed on Jul. 7, 2020 entitled “PREEMPTIBLE-BASED SCAFFOLD HOPPING” byMason Victors et al., and assigned to the assignee of the presentapplication, the disclosure of which is hereby incorporated herein byreference in its entirety.

TECHNICAL FIELD

The present disclosure related to a method and apparatus for molecularscaffold hopping in a preemptible computing environment.

BACKGROUND

Molecular scaffold hopping, the switching from one chemical corestructure of a molecule to another molecule having a different chemicalcore structure, as facilitated by computer-aid searching, is widelyknown and used for drug discovery and medicinal chemistry. Often,molecular scaffold hopping involves starting from some small moleculeand finding other small molecules that have similar electrostatic andshape properties. The effort to find such molecules can be highlycomputing-intensive and therefore both time and financially expensiveendeavors.

BRIEF DESCRIPTION

Reference is now made to the following descriptions taken in conjunctionwith the accompanying drawings, in which:

FIG. 1 illustrates a flow diagram of an example embodiment of a methodof molecular scaffold hopping according to the principles of thedisclosure;

FIG. 2 illustrates a block diagram of an example apparatus embodiment ofthe disclosure, e.g., an apparatus to implement embodiments of themethod such as disclosed in the context of FIG. 1 ;

FIG. 3A presents an example 2D molecular formula of an example querymolecule; and

FIG. 3B presents an example ensemble of 3D conformers of the examplequery molecules presented in FIG. 3A.

SUMMARY

In one aspect, the disclosure provides a method of molecular scaffoldhopping. The method includes sending instructions, from an interface ofa scheduler computer to a job runner computer, the instructions preparedby a processor of the scheduler computer, to perform a plurality ofseparate computational tasks, wherein each of the separate computationaltasks includes calculating one or more chemical properties for a querymolecule or for molecules in a library of molecules, wherein one or moreof the plurality of separate computational tasks performed on the jobrunner computer are preemptible computing instances. The method furtherincludes receiving status indicators, by the interface, the statusindicators sent from the job runner computer, for each of the pluralityof separate computational tasks, wherein each of the status indicatorsare one of: an incomplete computing instance, a completed computinginstance or a failed computing instance. The method also includesresending to the job runner computer by the interface, the instructionsto the job runner computer that correspond to the separate computationaltasks having the one status indicator of the failed computing instanceto thereby increase fault-tolerance against the one or more of theplurality of separate computational tasks not attaining the statusindicator of the completed computing instance.

In another aspect the disclosure provides for an apparatus for molecularscaffold hopping. The apparatus includes a scheduler computer includinga processor and an interface. The processor is configured to prepareinstructions to perform a plurality of separate computational tasks,wherein each of the separate computational tasks includes calculatingone or more chemical properties for a query molecule or for molecules ina library of molecules, wherein one or more of the plurality of separatecomputational tasks are preemptible computing instances. The interfaceis configured to send the instructions to a job runner computer, andreceive from the job runner computer, a status indicator of each of theplurality of separate computational tasks, wherein the status indicatoris one of an incomplete computing instance, a completed computinginstance or a failed computing instance. The interface is alsoconfigured to resend to the job runner computer, the instructions thatcorrespond to the separate computational tasks having the statusindicator of the failed computing instance to thereby increasefault-tolerance against the one or more of the plurality of separatecomputational tasks not attaining the status indicator of the completedcomputing instance.

DETAILED DESCRIPTION

We disclose herein a method and apparatus for performing molecularscaffold hopping on a large scale and in a time- and cost-efficientmanner by using a preemptible computing environment.

Preemptible computing refers to a non-reserved use of a plurality ofcomputers, e.g., computing cores in a cloud computing environment, toperform a series of computational tasks, or jobs. However, some or allof the computational tasks can be pre-empted by a reserved use of thesame computers to perform different computational tasks or jobs.Reserved computing refers to the reserved use of the plurality ofcomputers for as long as needed to perform and finish a series ofcomputational tasks before releasing the computing resource for othercomputational tasks.

Because the discounted fee for preemptible computing can be severaltimes lower than the fee for reserved computing, it was desirable forour molecular scaffold hopping computations to be carried out in apreemptible computing environment instead of a reserved computingenvironment. However several problems had to be overcome.

One problem is that when a preemptible computational task getspreempted, e.g., by a reserved computing task, then the preemptiblecomputational task can be ‘killed’, or terminated, and the task simplydisappears, with no partial results being saved and no notice that thetask has been killed. In some systems a signal notifying that the taskwill preempted in a short period (e.g., 30 s) may be given. Because noresults are obtained from the preemptible computational task up to thepoint of being killed the entire task has to be repeated from thebeginning, resulting in added time and costs. And, if multiple instancesof such preemptible computational tasks are killed, then the logisticaltime and effort for an individual to investigate and keep track of whichtasks were completed and which tasks were killed and therefore needs tobe repeated, adds to the time and cost for a molecular scaffold hoppingcomputation to be completed.

Another problem is that preemptible computational task can fail forother reasons than being pre-empted and killed by instances of reservedcomputing tasks. For instance, there can be a loss in communications,e.g., due to an internet failure, or other network partition, betweenthe computers performing the computational tasks and/or a computersending information needed perform the tasks or receiving informationdescribing the results of completed tasks. For instance, if the computersending information receives too many requests at about the same timethen that computer can crash.

To address these problems, our idea was to increase the fault-toleranceof molecular scaffold hopping in a preemptible computing environment bydeveloping a method and apparatus to divide the computational tasks formolecular scaffold hopping into a plurality (e.g., thousands or tens ofthousands) of small preemptible computing tasks, which each take a shortenough period (e.g., minutes) to complete to have a high probability ofcompleting before failure. Another idea was for our method and apparatusto include automated computer monitoring of the status of each of thecomputational tasks and retry any of the computational tasks that failedto complete within a configurable number of times as further disclosedbelow.

One embodiment of the disclosure is a method of molecular scaffoldhopping.

FIG. 1 illustrates a flow diagram of an example embodiment of a method100 of molecular scaffold hopping according to the principles of thedisclosure. FIG. 2 illustrates a block diagram of an example apparatus200 embodiment of the disclosure, e.g., an apparatus to implementembodiments of the method such as disclosed in the context of FIG. 1 .

With continuing reference to FIGS. 1-2 throughout, as illustrated, themethod 100 includes sending instructions (e.g., step 105), from aninterface of a scheduler computer (e.g., interface 205 of schedulercomputer 210) to a job runner computer (e.g., a job runner computer 215having one or more computing cores 217). The instructions are preparedby a processor of the scheduler computer (e.g., processor 220), toperform a plurality of separate computational tasks, each of theseparate computational tasks including calculating one or more chemicalproperties for a query molecule or for molecules in a library ofmolecules. One or more of the plurality of separate computational tasksperformed on the job runner computer are preemptible computinginstances.

The method 100 includes receiving status indicators, by the interface205 sent from the job runner computer 215, (e.g., step 110). The statusindicators, sent from the job runner computer, are for each of theplurality of separate computational tasks. Each of the status indicatorsare one of: an incomplete computing instance, a completed computinginstance or a failed computing instance.

The method 100 includes resending to the job runner computer 215 by theinterface 205 (e.g., step 115), the instructions to the job runnercomputer that correspond to the separate computational tasks having theone status indicator of the failed computing instance, to therebyincrease fault-tolerance against the one or more of the plurality ofseparate computational tasks not attaining the status indicator of thecompleted computing instance.

The term separate computational task refers to the computer computationor calculation of the one or more chemical properties query molecule orset of molecules, e.g., including calculations necessary to filter setsof molecules by molecular properties, including molecular weight,enumerate stereoisomers, creating 3D conformer ensembles of themolecules, calculate 2D molecular formulas and fingerprints, indexingthe set of molecules for fast searching and then for a query molecule,computing query molecule's chemical property similarity to the set ofmolecules as further described below.

Referring to the status indicators, a completed computing instancerefers to where the job runner computer has finished calculating the oneor more chemical properties and the job runner computer has stopped thecomputational task. An incomplete computing instance refers where thejob runner computer has not finished calculating the one or morechemical properties and the job runner computer is still running thecomputational task. A failed computing instance refers to where there isneither an incomplete computing instance nor a completed computinginstance associated with the computational task.

The term preemptible computing instances refers to any computinginstance which can be replaced, at any time, by reserved computinginstances operating on the job runner computer or other system event(e.g., due to system maintenance) or after a fixed time count (e.g., a24-hour or other fixed-time counter) that is allowed on the job runnercomputer.

The term increase fault-tolerance refers to the ability of the disclosedmethod and apparatus embodiments, with no human intervention, toautomatically resend the instruction to repeat any of the separatecomputational tasks until all of the separate computational tasks have astatus indicator equal to a completed computing instance. In someinstances, however, a status indicator equal to a failure can still beobtained for a separate computational task even after a configurablenumber and timing of resends of the task, according to step 115, e.g.,(e.g., two to 100 resends over the course of several minutes of hours oftimings).

The molecules in the library of molecule refer to a collection ofmolecules that are readily synthesizable, e.g., by a chemistry vendor,and, that are been selected for having drug-like properties (e.g., knownor thought to have a physiological effect on living cells).

The term query molecule refers to a theoretical molecule, a newlysynthesized molecule, or an existing molecule, which is hypothesized orknown to have drug-like properties for a target disease. E.g., the querymolecule can be any kind of molecule that is desired to be compared tothe molecules of the library.

In some embodiments of the method, to facilitate minimizingcomputational resources and network communication time, the resending ofthe instructions (step 115) does not include the instructionscorresponding to the separate computational tasks having the statusindicator equal to the incomplete computing instance or equal to thecomplete computing instance. E.g., the instruction resent in step 115include only the instructions corresponding to the computational taskhaving the failed computing instance status indicator.

In some embodiments, to further increase fault tolerance, as part ofstep 115 the resending of the instructions further includes an iterationinstruction (step 120) to repeat the resending of the instruction for aplurality of times for the separate computational tasks continuing tohave the one status indicator of the failed computing instance. E.g.,the scheduler computer 210 can configure the instructions sent by theinterface 205 in step 115 to include a plurality of repeat instances forrepeating the resending the instructions with a wait-time between eachresend instruction in accordance with step 120. Thus, for suchembodiments, the one computational task would have to have multipleconsecutive failure status indicators spend across a period of time(e.g., 5 minutes to hours) during which the preemptible computingresources of the job runner computer are engaged. However to avoidpossibility of an endless iteration loop or excessive computingresources, the number of repeat instance can be limited to a finitenumber (e.g., 2, 5, 10, 100 repeat instances).

In some embodiments, to minimize computing costs, all of the separatecomputational tasks performed on the job runner computer as instructedin step 110 are preemptible computing instances. However, in someembodiments one or more of the separate computational tasks can bedesignated to be performed on the job runner computer as reservedcomputing instances.

In some embodiments, to provide a broad range of fault tolerance, thefailed computing instance can occur due to one or more of: a preemptionof at least one of the separate computational tasks; a network partitionbetween the scheduler computer and the job runner computer; a networkpartition between the job runner computer and a resource computer (e.g.,FIG. 2 , resource computer 225) that includes a digital record ofchemical information (e.g., the chemical information recorded onnon-transitory digital data storage media 230) about the query moleculeor the molecules in the library of molecules; or an excess number ofinformation requests from the job runner computer to a resource computerthat includes a digital record of chemical information about the querymolecule or the molecules in the library of molecules.

In some embodiments, to reduce the time required for each of theseparate computational tasks to complete, e.g., before being preemptedby a reserved computing instance, the instructions sent from theinterface of the scheduler computer to the job runner computer as partof step 105 can include instructions to divide the plurality of separatecomputational tasks into portions divided that are completed in anaverage completion time that is less than an average preemption time forthe one or more of the separate computational instances. The division ofthe tasks into portions can be specified by a user and incorporated bythe processor 220 into the instructions sent to the job runner computer215 by the interface. For instance, in some such embodiments, theportions of the plurality of separate computational tasks includescalculating the one or more chemical properties for distinct subsets ofthe molecules in the library of molecules. E.g., each of the distinctsubsets of the molecules in the portions can be a collection rangingfrom 1/10000 to 1/10 of different ones of the molecule of a total numberof the molecule in the library of molecules. E.g., in some embodiments,if the total number of the molecule in the library of molecules equals 1billion molecules, then each of the distinctive subsets can range from100,000 to 100,000,000 molecules.

In some embodiments, to increase fault tolerance, the instructions sentfrom the interface of the scheduler computer to the job runner computeras part of step 105 can include instructions to initiate performing atleast two of the separate computational tasks at different times fromeach other. For instance, as noted elsewhere herein, one cause of afailure occurs because there are too many requests sent in a givenamount of time, e.g., too many concurrent requests or nearly concurrentrequests sent to an external service computer, e.g., for packets ofinformation related to the chemical data, from the multiple job runnercomputer because there is too much traffic. To help prevent this thescheduler computer can control the sending out of computational tasksout to the job runner computer at slight intervals or delay times. Thus,while the separate computational tasks, once running, can run inparallel, the individual separate computational tasks can each start atdifferent times at slightly different times than each other. E.g., insome embodiments, the scheduler computer, to help avoid overwhelming thejob runner computer, can queue up the separate computational tasksand/or start or run a configurable limited number of the tasks at thesame time. E.g., in some embodiments, the initiating of performing eachof the separate computational tasks can be sequential in time. E.g., insome embodiments, a delay time can be set between the initiating ofperforming a first one of the separate computational tasks and theinitiating of performing a second one of the separate computationaltasks. E.g., the delay time can be set to a value (e.g., 1, 2, 5, 10, 60seconds) that is greater than an average time for the job runnercomputer to access a resource computer that includes a digital record ofchemical information about the query molecule or the molecules in thelibrary of molecules.

Similarly, in some embodiments, the resending of the instructionscorresponding to the separate computational task having the one statusindicator equal to the failed computing instance, in accordance withstep 115, can further includes instructions to initiate performing atleast two of the separate computational tasks of such failed computinginstances at different times from each other.

Various strategies can be adopted in the method to facilitate theefficient computing of chemical properties and thereby improve faulttolerance.

In some embodiments, the separate computational tasks to calculate theone or more chemical properties can include molecular weight filteringof the molecules in the library of molecules to select a subset libraryof molecules that are within a multiplier of a molecular weight of thequery molecule can be adjusted to different ranges to narrow or expandthe size of the subset library of molecules, e.g., the multiplier of themolecular weight of the query molecule can be in a range from 3/4 to 5/4times, 1/2 to 2 times, 1/3 to 3 times, 1/4 to 4 times, or othercombinations thereof.

In some embodiments, the separate computational tasks to calculate theone or more chemical properties includes calculating an ensemble of 3Dconformers of the query molecule or of the molecules in the library. Insome such embodiments, at least 5, 7 or 10 and not more than 10, 15, or20 3D conformers, respectively, are calculated for each of the querymolecule and the molecules in the library. As a non-limiting example,FIG. 3A presents an example 2D molecular formula of an example querymolecule and FIG. 3B presents an example ensemble 3D conformers of theexample query molecules presented in FIG. 3A.

In some such embodiments, an energy window between any pair of 3Dconformers in the ensemble of 3D conformers is less than 5 kcal. Theterm energy window as used herein means the difference in relativeenergy between a conformer and the conformer with minimum energy for aquery molecule. In some embodiments, the energy window can be computedby calculating the energies of each conformer in an ensemble ofconformers via Merck Molecular Force Fields, identifying the conformerwith minimum relative energy (relative to the other conformers in theensemble). In some embodiments, restricting conformer ensembles to anenergy window of, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20 kcalhelps to avoid unrealistic conformations being included in the ensemble.

In some embodiments, the separate computational tasks to calculate theone or more chemical properties includes calculations to align one ofthe 3D conformers of the query molecule with one of the 3D conformers ofone of the molecules in the library of molecules to form an alignedconformer pair having a minimized molecular volumes difference andinclude calculating a Tanimoto shape similarity score representative ofthe minimized molecular volumes difference (e.g., a score of 0 to 1 onan arbitrary scale) as familiar to those skilled in the art. In somesuch embodiments, the separate computational tasks to calculate the oneor more chemical properties further includes calculating anelectrostatic charge difference map for the aligned conformer pairs andcalculating a Tanimoto charge similarity score representative of theelectrostatic charge difference map (e.g., e.g., a score of 0 to 1 on anarbitrary scale) as familiar to those skilled in the art.

In some such embodiments, the separate computational tasks to calculatethe one or more chemical properties further includes adding the Tanimotoshape similarity score and the Tanimoto charge similarity score togetherto give a combined Tanimoto shape-electrostatic similarity score (e.g.,a combined score of 0 to 2). As understood by those skilled in the art,a user can specify a threshold score for how similar a molecule has tobe in order to be returned as a hit (e.g., a molecule with similar shapeand electrostatic as the query molecule charge having a combined scoresequal to or greater than 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8 or 1.9),or, the user can specify the maximum number of molecules to be returnedwith the highest scores without specifying a particular threshold score.

In some embodiments, the separate computational tasks to calculate theone or more chemical properties includes calculating a 2D molecularfingerprint difference between the query molecule and one of themolecules of the library of molecules, and, calculating a Tanimotomolecular fingerprint similarity score representative of the 2Dmolecular fingerprint difference (e.g., a score of 0 to 1 on anarbitrary scale) as familiar to those skilled in the art. One skilled inthe pertinent art would be familiar with the calculation of molecularfingerprints, e.g., to make a vector, or other mathematical object,representation of a molecular structure to facilitate numericallyencoding structural information about the molecular structure. In somesuch embodiments, to help ensure that the molecules selected from themolecules of the library have different chemical core structures fromthat of the query molecule, the user may specify that the Tanimotomolecular fingerprint similarity score be low (e.g., 0.1 or less, 0.2 orless, 0.3 or less, 0.4 or less or 0.5 or less).

In some embodiments, the selection criterion for finding suitablemolecular scaffold hopping candidates might be those molecules from thelibrary of molecules where the combined Tanimoto shape-electrostaticsimilarity score is high (e.g., equal to or greater than 1.5) and theTanimoto molecular fingerprint similarity score is low (e.g., equal toor less than 0.2). Thus, the dual filters of Tanimotoshape-electrostatic similarity score and Tanimoto molecular fingerprintsimilarity score facilitate identifying molecules with conformer andcharge similarity but highly different chemical structural compositionsthan the query molecule.

As illustrated in FIG. 1 , the method 100 can further includes for eachone of the separate computational tasks attaining the status indicatorequal to the completed computing instance, sending from the job runnercomputer to the scheduler computer, notice of results of the separatecomputational task (step 125). For instance, the notice of results ofthe tasks could include a listing of the molecules from the library ofmolecules having a suitable Tanimoto shape-electrostatic similarityscore and Tanimoto molecular fingerprint similarity score as compared tothe query molecule. In some embodiments, the instructions (step 105)sent to the job runner computer include instructions on where to sendthe results of the completed computing instance (e.g., to the schedulercomputer 210, a resource computer 225 or other computer).

Another embodiment is an apparatus for molecular scaffold hopping, e.g.,to implement any of the embodiments of the method. Again with continuingreference to FIGS. 1-2 throughout, embodiments of the apparatus 200include a scheduler computer 210, the scheduler computer including aprocessor 220 and an interface 205. The processor can be configured toprepare instructions to perform a plurality of separate computationaltasks. Each of the separate computational tasks includes calculating oneor more chemical properties for a query molecule or for molecules in alibrary of molecules, where one or more, or sometimes all, of theplurality of separate computational tasks can be preemptible computinginstances. The interface can be configured to: send the instructions toa job runner computer: receive, from the job runner computer, a statusindicator of each of the plurality of separate computational tasks (oneof an incomplete computing instance, a completed computing instance or afailed computing instance); and resend to the job runner computer, theinstructions that correspond to the separate computational tasks havingthe status indicator of the failed computing instance, therebyincreasing fault-tolerance against the one or more of the plurality ofseparate computational tasks not attaining the status indicator of thecompleted computing instance.

In some embodiments, the scheduler computer processor 220 can receive arequest (e.g., from a user or automated user) to run the separatecomputational tasks to calculate the one or more chemical properties fora query molecule or for molecules in a library of molecules. Thescheduler computer sends instructions (step 105) via the interface 205to start the tasks running on job runner computer 215. In someembodiments, each of the separate computational tasks can be assigned todifferent computing cores 217 of the job runner computer 215. In someembodiments, upon receiving the instructions, each of the computingcores 217, can poll the scheduler computer 220 for its assigned separatecomputational tasks and when there are no more tasks then each computingcore 217 can terminate itself.

In some embodiments, the apparatus can be part of a computing system(e.g., system 250) that also includes the job runner computer.

In some embodiments, the instructions prepared by the processor and sentby the interface can include an iteration instruction to repeat theresending of the instruction for a plurality of times for the separatecomputational tasks continuing to have the one status indicator of thefailed computing instance.

In some embodiments, the processor can be configured (e.g., via adigital programming language) to prepare the instructions based ondividing the plurality of separate computational tasks into portionsthat are completed in an average completion time that is less than anaverage preemption time for the one or more of the separatecomputational instances.

In some embodiments, the instructions prepared by the processor and sentby the interface include instructions initiate performing at least twoof the separate computational tasks at different times from each other.

In some embodiments, the instructions prepared by the processor and sentby the interface include instructions for the resending of theinstructions, corresponding to the separate computational task havingthe status indicator equal to the failed computing instance, includefurther instructions to initiate performing at least two of the separatecomputational tasks at different times from each other.

In some embodiments, at least one the separate computational tasks tocalculate the one or more chemical properties includes molecular weightfiltering of the molecules in the library of molecules to select asubset library of molecules that are within a multiplier of a molecularweight of the query molecule. In some embodiments, at least one of theseparate computational tasks to calculate the one or more chemicalproperties includes calculating an ensemble of 3D conformers of thequery molecule or of the molecules in the library. In some embodiments,at least one the separate computational tasks to calculate the one ormore chemical properties includes calculations to align one of the 3Dconformers of the query molecule with one of the 3D conformers of one ofthe molecules in the library of molecules to form an aligned conformerpair having a minimized molecular volumes difference and calculating aTanimoto shape similarity score representative of the minimizedmolecular volumes difference. In some embodiments, at least one of theseparate computational tasks to calculate the one or more chemicalproperties includes calculating a 2D molecular fingerprint differencebetween the query molecule and one of the molecules of the library ofmolecules, and, calculating a Tanimoto molecular fingerprint similarityscore representative of the 2D molecular fingerprint difference.

In some embodiments, the instructions prepared by the processor and sentby the interface include instructions for the job runner computer tosend results of the separate computational tasks to the interface, foreach one of the separate computational tasks that attains the statusindicator equal to the completed computing instance.

Some embodiments of the apparatus 100 include a resource computer 225configured to store chemical information about the library of moleculesor query molecule in non-transitory storage media 230 and provide suchinformation when requested by the job runner computer 215 or computingcores of the job runner computer. In some embodiments, the resourcecomputer 225 or non-transitory storage media 230 can be part of thescheduler computer 210. In other embodiments, the scheduler computer 210can have separate non-transitory storage media 230 a, e.g., used forkeeping track of the separate computational, tasks such as which of thetasks are waiting to run, running, failed or completed. The job runnercomputer 215 or its computing cores 217 can include separate storagemedia to store input data obtained from the resource computer 225 andoutput data.

The interface 205 includes the necessary circuitry, components,firmware, software, etc., to transmit and receive data as aninput/output interface. The interface 205 can be a conventionalinterface associated with the processor 220 to communicate dataaccording to different standard protocols, such as industry orproprietary protocols used for communicating data between computingdevices. The interface 205 can be configured to communicate via acommunications network (e.g., network 222) when remotely located fromthe job runner computer 215, such as when the job runner computer iscloud-based. The communications network 222 can be a conventionalcommunications network that communicates via standard protocols.

In some embodiments, the job runner computer 215 can be or include asingle computer with one or more computing cores 217 (e.g., a pluralityof GPUs and/or CPUs) or each of the computing cores 217. In someembodiments, the job runner computer 215 can include one or moreindividual computers configured as virtual machines or computingclusters located proximate each other, or in a cloud environment, in adata center, or a combination thereof.

The processor 220 can be configured to control the operation of thescheduler computer 210 and interface 205. The processor 220, forexample, can include the necessary logic circuitry embodied in digitaldata processors such as CPU or GPUs, to store executable programs orsoftware instruction and to send and receive digital information to andfrom the interface 205.

In some embodiments, a user 240 (e.g., a human or automated process) caninteract with the scheduler computer 210 via the interface 205, bysubmitting or monitoring the separate computational tasks.

Those skilled in the art to which this application relates willappreciate that other and further additions, deletions, substitutionsand modifications may be made to the described embodiments.

What is claimed is:
 1. A method of molecular scaffold hopping,comprising: sending instructions, from an interface of a schedulercomputer to a job runner computer, the instructions prepared by aprocessor of the scheduler computer, to perform a plurality of separatecomputational tasks, wherein each of the separate computational tasksincludes calculating one or more chemical properties for a querymolecule or for molecules in a library of molecules, wherein one or moreof the plurality of separate computational tasks performed on the jobrunner computer are preemptible computing instances, wherein theseparate computational tasks to calculate the one or more chemicalproperties includes calculating an ensemble of 3D conformers of thequery molecule or of the molecules in the library, and further includescalculations to align one of the 3D conformers of the query moleculewith one of the 3D conformers of one of the molecules in the library ofmolecules to form an aligned conformer pair having a minimized molecularvolumes difference and calculating a Tanimoto shape similarity scorerepresentative of the minimized molecular volumes difference; receivingstatus indicators, by the interface, the status indicators sent from thejob runner computer, for each of the plurality of separate computationaltasks, wherein each of the status indicators are one of: an incompletecomputing instance, a completed computing instance, or a failedcomputing instance; and resending to the job runner computer by theinterface, the instructions to the job runner computer that correspondto the separate computational tasks having the one status indicator ofthe failed computing instance to thereby increase fault-toleranceagainst the one or more of the plurality of separate computational tasksnot attaining the status indicator of the completed computing instance.2. The method of claim 1, wherein the resending of the instructions doesnot include the instructions corresponding to the separate computationaltasks having the status indicator equal to the incomplete computinginstance or equal to the complete computing instance.
 3. The method ofclaim 1, wherein the resending of the instructions further includes aniteration instruction to repeat the resending of the instruction for aplurality of times for the separate computational tasks continuing tohave the one status indicator of the failed computing instance.
 4. Themethod of claim 1, wherein all of the separate computational tasksperformed on the job runner computer are preemptible computinginstances.
 5. The method of claim 1, wherein the failed computinginstance occurs due to one or more of: a preemption of at least one ofthe separate computational tasks; a network partition between thescheduler computer and the job runner computer; a network partitionbetween the job runner computer and a resource computer that includes adigital record of chemical information about the query molecule or themolecules in the library of molecules; or an excess number ofinformation requests from the job runner computer to a resource computerthat includes a digital record of chemical information about the querymolecule or the molecules in the library of molecules.
 6. The method ofclaim 1, wherein the instructions sent from the interface of thescheduler computer to the job runner computer include instructions toinitiate performing at least two of the separate computational tasks atdifferent times from each other.
 7. The method of claim 1, wherein theseparate computational tasks to calculate the one or more chemicalproperties includes molecular weight filtering of the molecules in thelibrary of molecules to select a subset library of molecules that arewithin a multiplier of a molecular weight of the query molecule.
 8. Themethod of claim 1, wherein the separate computational tasks to calculatethe one or more chemical properties includes calculating a 2D molecularfingerprint difference between the query molecule and one of themolecules of the library of molecules, and, calculating a Tanimotomolecular fingerprint similarity score representative of the 2Dmolecular fingerprint difference.
 9. An apparatus for molecular scaffoldhopping, the apparatus comprising: a scheduler computer, the schedulercomputer including a processor and an interface, wherein: the processoris configured to prepare instructions to perform a plurality of separatecomputational tasks, wherein each of the separate computational tasksincludes calculating one or more chemical properties for a querymolecule or for molecules in a library of molecules, wherein one or moreof the plurality of separate computational tasks are preemptiblecomputing instances, wherein the separate computational tasks tocalculate the one or more chemical properties includes calculating anensemble of 3D conformers of the query molecule or of the molecules inthe library, and further includes calculations to align one of the 3Dconformers of the query molecule with one of the 3D conformers of one ofthe molecules in the library of molecules to form an aligned conformerpair having a minimized molecular volumes difference and calculating aTanimoto shape similarity score representative of the minimizedmolecular volumes difference and the interface is configured to: sendthe instructions to a job runner computer, receive from the job runnercomputer, a status indicator of each of the plurality of separatecomputational tasks, wherein the status indicator is one of: anincomplete computing instance, a completed computing instance, or afailed computing instance, and resend to the job runner computer, theinstructions that correspond to the separate computational tasks havingthe status indicator of the failed computing instance to therebyincrease fault-tolerance against the one or more of the plurality ofseparate computational tasks not attaining the status indicator of thecompleted computing instance.
 10. The apparatus of claim 9, wherein theapparatus is part of a computing system that also includes the jobrunner computer.
 11. The apparatus of claim 9, wherein the instructionsprepared by the processor and sent by the interface includes aniteration instruction to repeat the resending of the instruction for aplurality of times for the separate computational tasks continuing tohave the one status indicator of the failed computing instance.
 12. Theapparatus of claim 9, wherein the instructions prepared by the processorand sent by the interface include instructions initiate performing atleast two of the separate computational tasks at different times fromeach other.
 13. The apparatus of claim 9, wherein at least one theseparate computational tasks to calculate the one or more chemicalproperties includes molecular weight filtering of the molecules in thelibrary of molecules to select a subset library of molecules that arewithin a multiplier of a molecular weight of the query molecule.
 14. Theapparatus of claim 9, wherein at least one of the separate computationaltasks to calculate the one or more chemical properties includescalculating a 2D molecular fingerprint difference between the querymolecule and one of the molecules of the library of molecules, and,calculating a Tanimoto molecular fingerprint similarity scorerepresentative of the 2D molecular fingerprint difference.